--------------------QDIFFXS------------------------ * * * a program to solve the P-B equation * * in 3D, using non-linear form, incorporating * * 2 dielectric regions, ionic strength, periodic * * and focussing boundary conditions, utilizing * * stripped optimum successive over-relaxation * * and surface charge position correction * * * --------------------QDIFFXS------------------------ program run on 28-Jun-04 at 15:22:08 parameters read from file ./ Q../ - Q dE grid size : 65 percent of box to be filled: 66.00000 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 80.00000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.800000 boundary conditions : coulombic x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : default parameters convergence graph turned off potential listings turned off initializing dielectric and debye maps... atom radii read from file fort.11 !my siz based on PARSE !(value for P taken from Pauling, ! for Mg from Biophys J 2001, 80, 1151) # of radius parameter records: 10 atomic charges read from file fort.12 !Amber parm94 charges # of charge parameter records: 732 assigning charges and radii... atomic coordinates, charges and radii written to file fort.19 box fill (%): 66.00000 xmin,xmax (A): 6000.000 -6000.000 ymin,ymax (A): 6000.000 -6000.000 zmin,zma (A): 6000.000 -6000.000 x,y,z range (A): -12000.00 -12000.00 -12000.00 scale (grids/A): -3.5200000E-03 object centre (A): 0.0000000E+00 0.0000000E+00 0.0000000E+00 time to read in and/or assign rad/chrg= 8.7756000E-02 number of atom coordinates read : 0 total number of charged atoms : 0 net assigned charge : 0.0000000E+00 assigned positive charge : 0.0000000E+00 centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 assigned negative charge : 0.0000000E+00 centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 time to turn everything out is 8.7848000E-02 number of grid points on expanded surface= 0 finishing off dielectric map... expanded surface maximum, minimum (g.u.)= 65 1 redo insides at 0.1691780 time to turn everything in is 0.1844010 number of dielectric boundary points 0 # grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.2178710 number of grid points assigned charge 0 setting boundary conditions... some initial phi values: midg,midg,1; midg,midg,igrid 0.0000000E+00 0.0000000E+00 midg,1,midg; midg,igrid,midg 0.0000000E+00 0.0000000E+00 1,midg,midg; igrid,midg,midg 0.0000000E+00 0.0000000E+00 gauss-seidel spectral radius is 2.2388822E-05 estimated iterations to convergence 11 setup time was (sec) 0.2877220 now iterating at: 15:22:09 rms-change max change #iterations 0.0000000E+00 0.0000000E+00 at 10iterations finished qdiffx linear iterations at : 15:22:09 time taken (sec) : 0.4704630 # loops : 10 mean,max change (kT/e) : 0.0000000E+00 0.0000000E+00 data file for analytic grid energy not present analytic grid energy is 0.0000000E+00 kt total energy (including grid energy): 0.0000000E+00 kt difference energy, in kcals, is 0.0000000E+00 number of unassigned boundary points= 0 number of membrane points scaled= 0 corrected reaction field energy: 0.0000000E+00 kt coulombic energy: 0.0000000E+00 kt energy calculations done at 0.4707790 frc stuff now done at 0.4708000 expanding potential and dielectric maps to full grid of 65... writing potential map in DELPHI format potential map written to file fort.14 setting up pointers... clearing bits... generating compact fine epsilon array... writing to compact epsilon file dielectric map written to file fort.17 total cpu time was (sec) 0.5182390 QDIFF QDIF. QDI.. QD... Q....